BioModels.net Web Services, a free and integrated toolkit for computational modelling software

Simple object access protocol (SOAP) is the communication protocol used by web services to communicate between systems. Since SOAP messages have the ability to bypass firewalls and directly get processed by web servers, their security is critical to the security of the web servers. Secure transit of SOAP messages plays a critical role for the applicability of web services. At present, internet users authenticate themselves using credential are vulnerable to security threats in presence of active attackers. This imposes a burden on users to manage their credentials in different ways. Along with the thorough development and application for web services, the security of it has taken people's attention more and more. While web services security (WSS) can exchange safe SOAP message and enhance the security of web services, it will also have certain influence to the performance of web services. This paper explore the security vulnerability of SOAP message transaction and taking advantage of the existing technologies and solutions related to SOAP and web services, we developing a highly developed security model. This model is useful for solving the problem between security and performance contradiction.

In this chapter, we provide an overview of the Web services technology, together with the set of standard specifications for Web services transactions. The core components of the Web services technology include eXtensible Markup Language (XML), HyperText Transfer Protocol (HTTP), Simple Object Access Protocol (SOAP), and Web Services Description Language (WSDL). Both SOAP and WSDL are based on XML. All these protocols and languages have the characteristic of strong extensibility, which lays a solid foundation for the success of the Web services technology. Due to the extensibility design, the protocols specified in the Web services transactions standards can be plugged into the Web services core seamlessly to provide the additional coordination needed for business transactions. Furthermore, we point out the need to protect the business transactions from the hardware failures and malicious faults, and for more robust coordination for Web services transactions.

This paper describes the proposed smart transducer Web services (STWS) developed at the National Institute of Standards and Technology (NIST) based on the IEEE 1451.0 standard. The STWS are described in WSDL (Web service description language). A prototype system has been established to test the STWS. This prototype system consists of a service consumer, service provider (wireless network node), and wireless sensor node. The service consumer and provider can communicate with each other through SOAP (simple object access protocol) messages. The STWS were tested successfully through a case study of reading an IEEE 1451 TEDS (transducer electronic data sheet). The proposed STWS provide a standard way for IEEE 1451 applications to achieve interoperability with other sensor applications in WSDL. Hence it provides a foundation for STWS standardization.

Web service is a technological solution for software interoperability that supports the seamless integration of diverse applications. In the vision of web service architecture, web services are described by the Web Service Description Language (WSDL), discovered through Universal Description, Discovery and Integration (UDDI) and communicate by the Simple Object Access Protocol (SOAP). Such a divination has never been fully accomplished yet. Although it was criticized that WSDL only has a syntactic definition of web services, but was not semantic, prior initiatives in semantic web services did not establish a correct methodology to resolve the problem. This paper examines the distinction and relationship between the syntactic and semantic definitions for web services that characterize different purposes in service computation. Further, this paper proposes that the semantics of web service are neutral and independent from the service interface definition, data types and platform. Such a conclusion can be a universal law in software engineering and service computing. Several use cases in the GIScience application are examined in this paper, while the formalization of geospatial services needs to be constructed by the GIScience community towards a comprehensive ontology of the conceptual definitions and relationships for geospatial computation. Advancements in semantic web services research will happen in domain science applications.

The advent of Web Services (WS) has signaled a true revolution in the way service-oriented computing and remote procedure invocation over the Web are conducted. Web Services comprise of a set of loosely coupled specifications to coordinate process execution from distance, based on common and widely accepted Web protocols such as HTTP, FTP, and XML, and therefore, providing increased development flexibility. Since the WS Framework was built on top of those protocols, Web Services have been widely acclaimed by the Web development community and paradoxically; they have marked one of the few examples in the history of computer protocols where a global consensus has been reached. The Web Service framework consists of essentially three basic components: 1. The Web Service Description Language (WSDL), a language that allows formal functional characterization of the provided functionalities; 2. The Simple Object Access Protocol (simply SOAP from its version 1.2), a protocol that defines the format of the information interchange; and 3. The UDDI (Universal Description, Discovery and Integration) is a catalog of Web Service descriptions. All three of these components are specified using XML markup. The elegance of the WS architecture lies in the fact that every WS transaction is taking place over established Web protocols such as HTTP and FTP. As remarked in Ballinger (2003, p. 5): “A Web Service is an application logic that is accessible using Internet standards.” This very fact has accounted for the rapid and universal adoption of Web Services. This work is organized as follows: First, a review of underlying technologies and tools is presented. Consequently, existing techniques for design methodologies are described. Next, an overview of storage and retrieval techniques for Web Services is given followed by real-world applications of Web Services. We conclude with open issues and discussion.

Chapter 11 - Web Services

A Web service is a software system that supports interoperable application-to-application interactions over a network. Web services are based on a set of XML standards such as Universal Description, Discovery and Integration (UDDI), Web Services Description Language (WSDL), and Simple Object Access Protocol (SOAP). Recently, there have been increasing demands and discussions about Web services privacy technologies in the industry and research community. To enable privacy protection for Web service consumers across multiple domains and services, the World Wide Web Consortium (W3C) published a document called “Web Services Architecture (WSA) Requirements” that defines some fundamental privacy requirements for Web services. However, no comprehensive solutions to the various privacy issues have been so far defined. For these reasons, this chapter will focus on privacy technologies by first discussing the main privacy issues in WSA and related protocols. Then, this chapter illustrates the standardization efforts going on in the context of privacy for Web services and proposes different technical approaches to tackle the privacy issues.

Softwareengineersareincreasinglyadoptingserviceorientedar-chitectures (SOAs) for the automation of business processes andthe integration of IT systems, both within and across organisa-tional boundaries. These service oriented architectures frequentlyrely on web service standards, such as the Web Service Descrip-tion Language (WSDL) [5] and the Simple Object Access Protocol(SOAP) [10] for the implementation of service invocations acrossmachine boundaries.The combination of several web services into a more complexweb service is a crucial building block for service oriented archi-tectures. Peltz refers to such compositions that integrate the in-vocation of two or more services into a more complex executableworkflow as web service orchestration and contrasts this with webservice choreography, which tracks message exchanges betweendifferent autonomous domains [13]. Web service orchestration isappealing as it facilitates compositionality and reuse of the compo-nents that implement these services without necessarily having todeploy these services locally.Web service orchestration is supported by the Business ProcessExecution Language for Web Services (BPEL) [1]. BPEL emergedthrough consolidation of earlier work on IBM’s Web Service FlowLanguage (WSFL) [11] and XLANG [14] developed by Microsoft.BPELwas proposedas astandardby Microsoft, IBM,Siebel, BEA

Web services are a technology that has gained enormous popularity in the industry over the past two years. Web services introduce a new paradigm in the field of distribute computing where the emphasis is on the protocol that’s used rather than how the technology is implemented. The main advantage Web services have over other technologies that support distributed computing is that Web services are based on open standards such as Extensible Markup Language (XML), Simple Object Access Protocol (SOAP), Web Services Description Language (WSDL), Hypertext Transfer Protocol (HTTP), and so on, and hence are widely accepted in the industry. More than any other distributed computing technologies in the past, Web services promote interoperability between heterogeneous and incompatible systems.

With the advent of distributed technologies and related Integrated Development Environments (IDEs), business collaborations across the world irrespective of the platforms in which applications were built.The underlying technology is Web Services which is based on XML standard and the architecture is SOA (Service Oriented Architecture).Many SOA frameworks came in to existence.However, their primary focus is discovering, composition of services in order to make flexible service oriented distributed enterprise applications.Such systems without human expertise may be incomplete.To overcome this problem, this paper proposes techniques to collaborate services based software with human experts thus forming a knowledgeintensive and people centric web besides sharing and reusing software components in distributed environment.To achieve this, we propose a flexible and adaptive approach which facilitates software services and humans to collaborate using Web Services and its important standards like SOAP (Simple Object Access Protocol), WSDL (Web Services Description Language) and UDDI (Universal Description Discovery Integration).This kind of human centric enterprise web has far reaching implications and it can attract the human experts to participate in rendering their best possible services.Interaction monitoring techniques that are adaptive thus realizing standards based people-centric systems.

Web services provide programmatic access to data or tools using internet technology. Several standards have been developed, one sophisticated application is the combination of the Web Service Description Language (WSDL) with the SOAP (originally defined as Simple Object Access Protocol) messaging protocol. We describe the fundamental technology of SOAP/WSDL-based web services and provide concepts to integrate data from independent, distant resources. Several informatics layers are described such as server-client messaging connections, programming languages, libraries, and modularity of web services. We illustrate principles underlying this technology and the types of web services they can be applied to in several functional stages, from simple data retrievals over combined data accesses (workflows) up to dynamically rendered images. As an example that is relevant for biomedicine we highlight the CancerResource as a use case for such diversified applications.The CancerResource is conceptualized to present cancerrelevant drug-target connections to the life sciences, particularly to the field of medical science. In-depth literature data-mining resolved thousands of drug-target connections. CancerResource connects manifold information from different knowledge categories. Targets are genes or proteins, which are well described in public databases like UniProt, Ensembl, and the PDB. Drugs are chemical compounds that specifically act on target genes in cancer tissues; they are collected in databases like DrugBank, SuperDrug, or PubChem. Connectivity Map (C-Map) expression data is an essential source of functional information for Cancer- Resource. A general visualization feature is the organization of genes in pathways; the KEGG database provides cancer-specific pathway maps. For this purpose CancerResource utilizes web service technologies to dynamically combine C-Map expression data with pathways. The CancerResource web interface allows the user to specify problems and helps to understand noticeable behaviors of genes that are implicated in cancer. The ultimate aim of CancerResource is to provide suggestions towards developing specific drug therapies for cancer patients.KeywordsSOAP/WSDLweb serviceinteroperabilitycancer medicinedrug treatment

The exploding number of computational models produced by Systems Biologists over the last years is an invitation to structure and exploit this new wealth of information. Researchers would like to trace models relevant to specific scientific questions, to explore their biological content, to align and combine them, and to match them with experimental data. To automate these processes, it is essential to consider semantic annotations, which describe their biological meaning. As a prerequisite for a wide range of computational methods, we propose general and flexible similarity measures for Systems Biology models computed from semantic annotations. By using these measures and a large extensible ontology, we implement a platform that can retrieve, cluster, and align Systems Biology models and experimental data sets. At present, its major application is the search for relevant models in the BioModels Database, starting from initial models, data sets, or lists of biological concepts. Beyond similarity searches, the representation of models by semantic feature vectors may pave the way for visualisation, exploration, and statistical analysis of large collections of models and corresponding data.

Chapter 7 - Writing SOAP Servers

This study develops the web services that are applied in home automation via the Internet and operated by mobile portable devices. Related work, a service-oriented architecture (SOA) platform is developed. Mobile portable devices are acting as Service-Requestor. A home appliance server is acting as Service-Provider. We use Web Services Description Language (WSDL) to describe their binding. The Simple Object Access Protocol (SOAP) provides a simple and lightweight protocol for communicating between them. An example is described in this study that includes a General Packet Radio Service (GPRS) control platform to provide the home gateway function.

Schema-driven Customization of Web Services